Variant report

Variant	rs13005148
Chromosome Location	chr2:99467538-99467539
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99466677..99468952-chr2:99480016..99482903,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10175560	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123756	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11900176	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11900524	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12467504	0.81[EUR][1000 genomes]
rs12478574	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712033	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs12712034	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12712037	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712039	0.86[ASN][1000 genomes]
rs12712040	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12990579	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13005124	0.86[CEU][hapmap]
rs13006398	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13024838	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13028500	0.87[CEU][hapmap]
rs1581249	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17758170	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1878589	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1949424	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1962029	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280142	0.90[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4311103	0.83[CEU][hapmap]
rs4499468	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4553869	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851174	0.82[CEU][hapmap]
rs4851175	0.86[CEU][hapmap]
rs6542837	0.90[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs6542839	0.83[GIH][hapmap];0.81[MEX][hapmap]
rs6542841	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704682	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6724477	0.91[CEU][hapmap];0.87[TSI][hapmap]
rs6739097	0.83[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs6741166	0.90[EUR][1000 genomes]
rs6752025	0.90[EUR][1000 genomes]
rs6755640	0.83[EUR][1000 genomes]
rs6757098	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760065	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7423519	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7565510	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7565614	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7565736	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7565819	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588441	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7590596	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7593332	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7608889	0.84[CEU][hapmap]
rs883773	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs885115	0.83[EUR][1000 genomes]
rs925887	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13005148	LIPT1	cis	cerebellum	SCAN
rs13005148	TSGA10	cis	multi-tissue	Pritchard
rs13005148	FAHD2B	cis	parietal	SCAN
rs13005148	LIPT1	cis	parietal	SCAN
rs13005148	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:99463400-99485400	Weak transcription	Gastric	stomach
5	chr2:99466000-99468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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